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I have a n3ds under Luma3DS Emu 11.0 firmware (Sysnand under 9.2 firmware).
My R4i SDHC RTS flashcart is well recognized on home desktop.
DS game are working well.
But after a game session, when I wish to exit flashcart, I need to push home button and then whole 3ds is reseting (like exiting settings parameters)
Hence the 3ds reboots and moreover, I then lost all the activity log relative to the use of this flashcart (like a game flashcart).
It is boring, is there a solution so as to exit DS flashcart and get back on emunand directly without rebooting the 3ds.

It's a known issue with flashcarts (gba and dsiware titles included) and the system settings app. CFW developers have yet to still figure it out!
A easy fix (but time consuming to install), although it may not solve your activity log issue, is to install A9LH if you are feeling comfortable with the process.

A9LH exploits your 3ds as soon as you turn it on, so when the 3ds exits the nds mode, it will attempt to reboot into sysnand only to be hacked to boot into either a luma3ds sysnand or emunand.

To solve your activity log issue, I suppose you need to use sysnand once you have installed A9LH. I am not totally sure.

I have my flashcard reboot into my emunand with A9LH.

Either way, A9LH should help you out? If you do decide to install the hax, PLEASE read over every aspect of the guide before attempting, including the caveats and potential issues. At no stage should you skip making NAND backups. If you brick (scary, ik) they will be your only saviour.

Thank you for your answer.
Yes, under sysnand, R4i flashcard works nice with activity log operational.
But, I prefer having to boot directly on my emunand with one complete activity log : homebrews, games are here
And with emunand you have no risk at all as I understood (except keep doing firmware update only through system settings).
It is like you were having linux and windows on the same PC : you can't imagine to reboot your pc to use a particular software you see...

Regardless of A9LH or Menuhax/Mset/OtherEntrypoints*HAX when the 3DS executes GBA/DS(DSi) code it reboots itself into TWL/AGB firms downclocking to act as a mere DS(i) or GBA with all other functions or powers disabled.

I have Menuhax (Lesshax) coldboot method and it autoboots into emunand every time with around 90% success rate. way less risky than a9lh imo.

This means that when you execute your flashcart in your emunand it will automatically reboot itself into SYSNAND_TWL_FIRM. Afaik, there is no known way to keep the log of your flashcart while opening it from emunand, it will save itself to sysnand.

It's not a matter of how the CFW works, but rather how the 3ds handles reboots. Which is certainly different with Flashcarts and GBA VC than on games that require a reboot upon exit (MH4U, Smash, MHX, System settings)

I don't think the other firms have been RE'd enough like to control or prevent this.

The activity log will show how many times you've executed the title, but showing 0:00 as playtime though.